Starting phenix.real_space_refine on Sat Jul 4 14:01:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cuj_45935/07_2026/9cuj_45935.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cuj_45935/07_2026/9cuj_45935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cuj_45935/07_2026/9cuj_45935.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cuj_45935/07_2026/9cuj_45935.map" model { file = "/net/cci-nas-00/data/ceres_data/9cuj_45935/07_2026/9cuj_45935.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cuj_45935/07_2026/9cuj_45935.cif" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.076 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 20 5.49 5 S 160 5.16 5 C 14288 2.51 5 N 3336 2.21 5 O 3752 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21557 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4895 Classifications: {'peptide': 610} Link IDs: {'PTRANS': 26, 'TRANS': 583} Chain: "B" Number of atoms: 4895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4895 Classifications: {'peptide': 610} Link IDs: {'PTRANS': 26, 'TRANS': 583} Chain: "C" Number of atoms: 4895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4895 Classifications: {'peptide': 610} Link IDs: {'PTRANS': 26, 'TRANS': 583} Chain: "D" Number of atoms: 4895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4895 Classifications: {'peptide': 610} Link IDs: {'PTRANS': 26, 'TRANS': 583} Chain: "A" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 476 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'PCW': 5, 'POV': 8, 'Y01': 3} Classifications: {'undetermined': 16} Link IDs: {None: 15} Chain breaks: 1 Unresolved non-hydrogen bonds: 315 Unresolved non-hydrogen angles: 384 Unresolved non-hydrogen dihedrals: 283 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-1': 1, 'POV:plan-2': 1, 'PCW:plan-1': 5, 'PCW:plan-3': 5, 'PCW:plan-4': 5, 'PCW:plan-2': 2} Unresolved non-hydrogen planarities: 78 Chain: "B" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 476 Unusual residues: {'PCW': 5, 'POV': 8, 'Y01': 3} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 315 Unresolved non-hydrogen angles: 384 Unresolved non-hydrogen dihedrals: 283 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-1': 1, 'POV:plan-2': 1, 'PCW:plan-1': 5, 'PCW:plan-3': 5, 'PCW:plan-4': 5, 'PCW:plan-2': 2} Unresolved non-hydrogen planarities: 78 Chain: "C" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 476 Unusual residues: {'PCW': 5, 'POV': 8, 'Y01': 3} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 315 Unresolved non-hydrogen angles: 384 Unresolved non-hydrogen dihedrals: 283 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'POV:plan-3': 2, 'POV:plan-1': 1, 'POV:plan-2': 1, 'PCW:plan-1': 5, 'PCW:plan-3': 5, 'PCW:plan-4': 5, 'PCW:plan-2': 2} Unresolved non-hydrogen planarities: 78 Chain: "D" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 476 Unusual residues: {'PCW': 5, 'POV': 8, 'Y01': 3} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 315 Unresolved non-hydrogen angles: 384 Unresolved non-hydrogen dihedrals: 283 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PCW:plan-1': 5, 'PCW:plan-3': 5, 'PCW:plan-4': 5, 'POV:plan-3': 2, 'POV:plan-1': 1, 'POV:plan-2': 1, 'PCW:plan-2': 2} Unresolved non-hydrogen planarities: 78 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "B" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Time building chain proxies: 4.00, per 1000 atoms: 0.19 Number of scatterers: 21557 At special positions: 0 Unit cell: (131.97, 131.97, 122.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 160 16.00 P 20 15.00 O 3752 8.00 N 3336 7.00 C 14288 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 600.1 milliseconds 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4608 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 8 sheets defined 67.3% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 28 through 47 removed outlier: 3.675A pdb=" N SER A 32 " --> pdb=" O SER A 28 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP A 45 " --> pdb=" O GLN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 Processing helix chain 'A' and resid 57 through 66 removed outlier: 3.546A pdb=" N LEU A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.578A pdb=" N VAL A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 106 removed outlier: 4.008A pdb=" N VAL A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 106' Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.752A pdb=" N VAL A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 removed outlier: 3.580A pdb=" N ARG A 134 " --> pdb=" O MET A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 173 removed outlier: 3.505A pdb=" N CYS A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 185 removed outlier: 3.590A pdb=" N HIS A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 204 through 206 No H-bonds generated for 'chain 'A' and resid 204 through 206' Processing helix chain 'A' and resid 208 through 222 removed outlier: 3.914A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.754A pdb=" N VAL A 235 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 250 removed outlier: 3.549A pdb=" N ALA A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY A 248 " --> pdb=" O PHE A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 291 through 299 removed outlier: 3.572A pdb=" N ILE A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 309 removed outlier: 3.844A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 324 removed outlier: 3.581A pdb=" N LEU A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 349 removed outlier: 3.652A pdb=" N TYR A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS A 346 " --> pdb=" O CYS A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 377 removed outlier: 4.067A pdb=" N TYR A 377 " --> pdb=" O LEU A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 404 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.867A pdb=" N PHE A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG A 409 " --> pdb=" O PRO A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 423 removed outlier: 4.415A pdb=" N THR A 419 " --> pdb=" O PHE A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 445 Processing helix chain 'A' and resid 450 through 463 removed outlier: 3.573A pdb=" N VAL A 459 " --> pdb=" O SER A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 470 removed outlier: 3.700A pdb=" N ALA A 469 " --> pdb=" O MET A 466 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 487 Processing helix chain 'A' and resid 489 through 512 removed outlier: 5.827A pdb=" N TRP A 495 " --> pdb=" O MET A 491 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 515 No H-bonds generated for 'chain 'A' and resid 513 through 515' Processing helix chain 'A' and resid 525 through 538 Processing helix chain 'A' and resid 552 through 566 removed outlier: 4.215A pdb=" N SER A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 588 removed outlier: 3.545A pdb=" N LEU A 574 " --> pdb=" O MET A 570 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 606 removed outlier: 3.575A pdb=" N ALA A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 removed outlier: 3.530A pdb=" N LEU A 612 " --> pdb=" O PRO A 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 47 removed outlier: 3.746A pdb=" N ASN B 37 " --> pdb=" O ARG B 33 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP B 45 " --> pdb=" O GLN B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 Processing helix chain 'B' and resid 57 through 66 removed outlier: 3.546A pdb=" N LEU B 61 " --> pdb=" O ASP B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.578A pdb=" N VAL B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 106 removed outlier: 4.009A pdb=" N VAL B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 106' Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.753A pdb=" N VAL B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 139 removed outlier: 3.579A pdb=" N ARG B 134 " --> pdb=" O MET B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 173 removed outlier: 3.506A pdb=" N CYS B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 185 removed outlier: 3.590A pdb=" N HIS B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 204 through 206 No H-bonds generated for 'chain 'B' and resid 204 through 206' Processing helix chain 'B' and resid 208 through 222 removed outlier: 3.914A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TYR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 removed outlier: 3.755A pdb=" N VAL B 235 " --> pdb=" O LEU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 250 removed outlier: 3.550A pdb=" N ALA B 247 " --> pdb=" O PRO B 243 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 291 through 299 removed outlier: 3.573A pdb=" N ILE B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 309 removed outlier: 3.844A pdb=" N LEU B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 324 removed outlier: 3.581A pdb=" N LEU B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 349 removed outlier: 3.652A pdb=" N TYR B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS B 346 " --> pdb=" O CYS B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 377 removed outlier: 4.067A pdb=" N TYR B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 404 Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.866A pdb=" N PHE B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG B 409 " --> pdb=" O PRO B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 423 removed outlier: 4.415A pdb=" N THR B 419 " --> pdb=" O PHE B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 445 Processing helix chain 'B' and resid 450 through 463 removed outlier: 3.574A pdb=" N VAL B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 470 removed outlier: 3.700A pdb=" N ALA B 469 " --> pdb=" O MET B 466 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 487 Processing helix chain 'B' and resid 489 through 512 removed outlier: 5.827A pdb=" N TRP B 495 " --> pdb=" O MET B 491 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 499 " --> pdb=" O TRP B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 515 No H-bonds generated for 'chain 'B' and resid 513 through 515' Processing helix chain 'B' and resid 525 through 538 Processing helix chain 'B' and resid 552 through 566 removed outlier: 4.215A pdb=" N SER B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 588 removed outlier: 3.544A pdb=" N LEU B 574 " --> pdb=" O MET B 570 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP B 580 " --> pdb=" O ALA B 576 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 606 removed outlier: 3.574A pdb=" N ALA B 595 " --> pdb=" O GLU B 591 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 613 removed outlier: 3.531A pdb=" N LEU B 612 " --> pdb=" O PRO B 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 47 removed outlier: 3.746A pdb=" N ASN C 37 " --> pdb=" O ARG C 33 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP C 45 " --> pdb=" O GLN C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 55 Processing helix chain 'C' and resid 57 through 66 removed outlier: 3.546A pdb=" N LEU C 61 " --> pdb=" O ASP C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.578A pdb=" N VAL C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 106 removed outlier: 4.007A pdb=" N VAL C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 106' Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.753A pdb=" N VAL C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 139 removed outlier: 3.581A pdb=" N ARG C 134 " --> pdb=" O MET C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 173 removed outlier: 3.505A pdb=" N CYS C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 185 removed outlier: 3.589A pdb=" N HIS C 185 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 203 Processing helix chain 'C' and resid 204 through 206 No H-bonds generated for 'chain 'C' and resid 204 through 206' Processing helix chain 'C' and resid 208 through 222 removed outlier: 3.914A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 235 removed outlier: 3.755A pdb=" N VAL C 235 " --> pdb=" O LEU C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 250 removed outlier: 3.549A pdb=" N ALA C 247 " --> pdb=" O PRO C 243 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLY C 248 " --> pdb=" O PHE C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 259 Processing helix chain 'C' and resid 291 through 299 removed outlier: 3.573A pdb=" N ILE C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 309 removed outlier: 3.843A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 324 removed outlier: 3.582A pdb=" N LEU C 316 " --> pdb=" O PRO C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 349 removed outlier: 3.651A pdb=" N TYR C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS C 346 " --> pdb=" O CYS C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 377 removed outlier: 4.067A pdb=" N TYR C 377 " --> pdb=" O LEU C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 404 Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.866A pdb=" N PHE C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG C 409 " --> pdb=" O PRO C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 423 removed outlier: 4.415A pdb=" N THR C 419 " --> pdb=" O PHE C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 445 Processing helix chain 'C' and resid 450 through 463 removed outlier: 3.573A pdb=" N VAL C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 470 removed outlier: 3.700A pdb=" N ALA C 469 " --> pdb=" O MET C 466 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 487 Processing helix chain 'C' and resid 489 through 512 removed outlier: 5.827A pdb=" N TRP C 495 " --> pdb=" O MET C 491 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 515 No H-bonds generated for 'chain 'C' and resid 513 through 515' Processing helix chain 'C' and resid 525 through 538 Processing helix chain 'C' and resid 552 through 566 removed outlier: 4.215A pdb=" N SER C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 588 removed outlier: 3.545A pdb=" N LEU C 574 " --> pdb=" O MET C 570 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP C 580 " --> pdb=" O ALA C 576 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU C 588 " --> pdb=" O ARG C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 606 removed outlier: 3.575A pdb=" N ALA C 595 " --> pdb=" O GLU C 591 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 613 removed outlier: 3.530A pdb=" N LEU C 612 " --> pdb=" O PRO C 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 47 removed outlier: 3.747A pdb=" N ASN D 37 " --> pdb=" O ARG D 33 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 Processing helix chain 'D' and resid 57 through 66 removed outlier: 3.546A pdb=" N LEU D 61 " --> pdb=" O ASP D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.577A pdb=" N VAL D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 106 removed outlier: 4.008A pdb=" N VAL D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 106' Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.752A pdb=" N VAL D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 removed outlier: 3.580A pdb=" N ARG D 134 " --> pdb=" O MET D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 173 removed outlier: 3.506A pdb=" N CYS D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 185 removed outlier: 3.589A pdb=" N HIS D 185 " --> pdb=" O LEU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 203 Processing helix chain 'D' and resid 204 through 206 No H-bonds generated for 'chain 'D' and resid 204 through 206' Processing helix chain 'D' and resid 208 through 222 removed outlier: 3.914A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 235 removed outlier: 3.754A pdb=" N VAL D 235 " --> pdb=" O LEU D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 250 removed outlier: 3.549A pdb=" N ALA D 247 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY D 248 " --> pdb=" O PHE D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 259 Processing helix chain 'D' and resid 291 through 299 removed outlier: 3.573A pdb=" N ILE D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 309 removed outlier: 3.843A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 324 removed outlier: 3.581A pdb=" N LEU D 316 " --> pdb=" O PRO D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 349 removed outlier: 3.651A pdb=" N TYR D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS D 346 " --> pdb=" O CYS D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 377 removed outlier: 4.067A pdb=" N TYR D 377 " --> pdb=" O LEU D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 404 Processing helix chain 'D' and resid 404 through 410 removed outlier: 3.866A pdb=" N PHE D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG D 409 " --> pdb=" O PRO D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 423 removed outlier: 4.415A pdb=" N THR D 419 " --> pdb=" O PHE D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 445 Processing helix chain 'D' and resid 450 through 463 removed outlier: 3.574A pdb=" N VAL D 459 " --> pdb=" O SER D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 470 removed outlier: 3.700A pdb=" N ALA D 469 " --> pdb=" O MET D 466 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 487 Processing helix chain 'D' and resid 489 through 512 removed outlier: 5.827A pdb=" N TRP D 495 " --> pdb=" O MET D 491 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 515 No H-bonds generated for 'chain 'D' and resid 513 through 515' Processing helix chain 'D' and resid 525 through 538 Processing helix chain 'D' and resid 552 through 566 removed outlier: 4.215A pdb=" N SER D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 588 removed outlier: 3.544A pdb=" N LEU D 574 " --> pdb=" O MET D 570 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP D 580 " --> pdb=" O ALA D 576 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU D 588 " --> pdb=" O ARG D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 606 removed outlier: 3.574A pdb=" N ALA D 595 " --> pdb=" O GLU D 591 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 613 removed outlier: 3.530A pdb=" N LEU D 612 " --> pdb=" O PRO D 609 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 268 removed outlier: 6.690A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AA3, first strand: chain 'B' and resid 265 through 268 removed outlier: 6.691A pdb=" N SER B 275 " --> pdb=" O GLN B 267 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 352 through 354 Processing sheet with id=AA5, first strand: chain 'C' and resid 265 through 268 removed outlier: 6.691A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 352 through 354 Processing sheet with id=AA7, first strand: chain 'D' and resid 265 through 268 removed outlier: 6.691A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 1010 hydrogen bonds defined for protein. 2922 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.87 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 3204 1.30 - 1.43: 5461 1.43 - 1.56: 12808 1.56 - 1.69: 175 1.69 - 1.81: 272 Bond restraints: 21920 Sorted by residual: bond pdb=" C29 POV A 803 " pdb="C210 POV A 803 " ideal model delta sigma weight residual 1.333 1.552 -0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C29 POV B 805 " pdb="C210 POV B 805 " ideal model delta sigma weight residual 1.333 1.552 -0.219 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C29 POV D 809 " pdb="C210 POV D 809 " ideal model delta sigma weight residual 1.333 1.551 -0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C29 POV C 805 " pdb="C210 POV C 805 " ideal model delta sigma weight residual 1.333 1.551 -0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" C29 POV C 808 " pdb="C210 POV C 808 " ideal model delta sigma weight residual 1.333 1.550 -0.217 2.00e-02 2.50e+03 1.17e+02 ... (remaining 21915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 28517 3.25 - 6.50: 676 6.50 - 9.75: 159 9.75 - 12.99: 68 12.99 - 16.24: 16 Bond angle restraints: 29436 Sorted by residual: angle pdb=" C GLU C 68 " pdb=" N ASP C 69 " pdb=" CA ASP C 69 " ideal model delta sigma weight residual 121.54 133.83 -12.29 1.91e+00 2.74e-01 4.14e+01 angle pdb=" C GLU A 68 " pdb=" N ASP A 69 " pdb=" CA ASP A 69 " ideal model delta sigma weight residual 121.54 133.82 -12.28 1.91e+00 2.74e-01 4.14e+01 angle pdb=" C GLU D 68 " pdb=" N ASP D 69 " pdb=" CA ASP D 69 " ideal model delta sigma weight residual 121.54 133.77 -12.23 1.91e+00 2.74e-01 4.10e+01 angle pdb=" C GLU B 68 " pdb=" N ASP B 69 " pdb=" CA ASP B 69 " ideal model delta sigma weight residual 121.54 133.77 -12.23 1.91e+00 2.74e-01 4.10e+01 angle pdb=" C29 POV A 806 " pdb="C210 POV A 806 " pdb="C211 POV A 806 " ideal model delta sigma weight residual 127.67 111.43 16.24 3.00e+00 1.11e-01 2.93e+01 ... (remaining 29431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.26: 13225 30.26 - 60.52: 696 60.52 - 90.78: 69 90.78 - 121.04: 14 121.04 - 151.30: 12 Dihedral angle restraints: 14016 sinusoidal: 6880 harmonic: 7136 Sorted by residual: dihedral pdb=" CA ASP C 69 " pdb=" C ASP C 69 " pdb=" N CYS C 70 " pdb=" CA CYS C 70 " ideal model delta harmonic sigma weight residual 180.00 153.16 26.84 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA ASP B 69 " pdb=" C ASP B 69 " pdb=" N CYS B 70 " pdb=" CA CYS B 70 " ideal model delta harmonic sigma weight residual 180.00 153.18 26.82 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA ASP A 69 " pdb=" C ASP A 69 " pdb=" N CYS A 70 " pdb=" CA CYS A 70 " ideal model delta harmonic sigma weight residual 180.00 153.19 26.81 0 5.00e+00 4.00e-02 2.87e+01 ... (remaining 14013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2767 0.074 - 0.148: 395 0.148 - 0.222: 30 0.222 - 0.296: 0 0.296 - 0.370: 12 Chirality restraints: 3204 Sorted by residual: chirality pdb=" CG LEU D 458 " pdb=" CB LEU D 458 " pdb=" CD1 LEU D 458 " pdb=" CD2 LEU D 458 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" CG LEU B 458 " pdb=" CB LEU B 458 " pdb=" CD1 LEU B 458 " pdb=" CD2 LEU B 458 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" CG LEU A 458 " pdb=" CB LEU A 458 " pdb=" CD1 LEU A 458 " pdb=" CD2 LEU A 458 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.38e+00 ... (remaining 3201 not shown) Planarity restraints: 3552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV B 805 " 0.299 2.00e-02 2.50e+03 2.99e-01 8.96e+02 pdb=" C29 POV B 805 " -0.297 2.00e-02 2.50e+03 pdb="C210 POV B 805 " -0.302 2.00e-02 2.50e+03 pdb="C211 POV B 805 " 0.299 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV D 809 " -0.292 2.00e-02 2.50e+03 2.93e-01 8.58e+02 pdb=" C29 POV D 809 " 0.288 2.00e-02 2.50e+03 pdb="C210 POV D 809 " 0.298 2.00e-02 2.50e+03 pdb="C211 POV D 809 " -0.294 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV A 803 " -0.287 2.00e-02 2.50e+03 2.90e-01 8.43e+02 pdb=" C29 POV A 803 " 0.278 2.00e-02 2.50e+03 pdb="C210 POV A 803 " 0.302 2.00e-02 2.50e+03 pdb="C211 POV A 803 " -0.293 2.00e-02 2.50e+03 ... (remaining 3549 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5834 2.81 - 3.33: 17911 3.33 - 3.86: 33584 3.86 - 4.38: 43816 4.38 - 4.90: 72872 Nonbonded interactions: 174017 Sorted by model distance: nonbonded pdb=" O ALA C 563 " pdb=" OG1 THR C 567 " model vdw 2.291 3.040 nonbonded pdb=" O ALA A 563 " pdb=" OG1 THR A 567 " model vdw 2.292 3.040 nonbonded pdb=" O ALA B 563 " pdb=" OG1 THR B 567 " model vdw 2.292 3.040 nonbonded pdb=" O ALA D 563 " pdb=" OG1 THR D 567 " model vdw 2.292 3.040 nonbonded pdb=" OE2 GLU A 535 " pdb=" O HOH A 901 " model vdw 2.312 3.040 ... (remaining 174012 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 28 through 637 or resid 806)) selection = (chain 'B' and (resid 28 through 637 or (resid 806 and (name C2 or name C21 or n \ ame C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name O21 or name O22 or name C210 or name C211 or name C212 or na \ me C213 or name C214 or name C215 or name C216)))) selection = (chain 'C' and (resid 28 through 637 or (resid 806 and (name C2 or name C21 or n \ ame C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name O21 or name O22 or name C210 or name C211 or name C212 or na \ me C213 or name C214 or name C215 or name C216)))) selection = (chain 'D' and (resid 28 through 637 or (resid 806 and (name C2 or name C21 or n \ ame C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 \ or name C29 or name O21 or name O22 or name C210 or name C211 or name C212 or na \ me C213 or name C214 or name C215 or name C216)))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 16.160 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.219 21920 Z= 0.533 Angle : 1.393 16.244 29436 Z= 0.640 Chirality : 0.054 0.370 3204 Planarity : 0.013 0.299 3552 Dihedral : 17.597 151.303 9408 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.51 % Allowed : 3.02 % Favored : 95.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.66 (0.11), residues: 2432 helix: -4.26 (0.06), residues: 1456 sheet: -2.58 (0.65), residues: 76 loop : -2.56 (0.17), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 589 TYR 0.027 0.003 TYR A 377 PHE 0.028 0.003 PHE B 169 TRP 0.027 0.003 TRP A 629 HIS 0.012 0.003 HIS C 522 Details of bonding type rmsd/Z covalent geometry : bond 0.01125 / 0.53 (21920) covalent geometry : angle 1.39314 / 0.64 (29436) hydrogen bonds : bond 0.33578 / 22.00 ( 1010) hydrogen bonds : angle 9.45382 / 6.44 ( 2922) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 500 time to evaluate : 0.506 Fit side-chains REVERT: A 47 SER cc_start: 0.6063 (m) cc_final: 0.5480 (p) REVERT: A 93 GLU cc_start: 0.6607 (mp0) cc_final: 0.6277 (mt-10) REVERT: A 96 MET cc_start: 0.5079 (mtm) cc_final: 0.4695 (mtm) REVERT: A 110 MET cc_start: 0.6739 (mtt) cc_final: 0.6473 (mtt) REVERT: A 139 ARG cc_start: 0.6568 (mtt-85) cc_final: 0.6211 (mpt180) REVERT: A 177 GLU cc_start: 0.7095 (mp0) cc_final: 0.6571 (mp0) REVERT: A 311 THR cc_start: 0.6079 (OUTLIER) cc_final: 0.5162 (m) REVERT: A 375 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7623 (mt-10) REVERT: A 379 THR cc_start: 0.7517 (t) cc_final: 0.7167 (p) REVERT: A 381 LYS cc_start: 0.7950 (mtmt) cc_final: 0.7566 (mtpt) REVERT: A 589 ARG cc_start: 0.7035 (tmm160) cc_final: 0.6758 (ttm-80) REVERT: A 590 ASP cc_start: 0.7399 (m-30) cc_final: 0.7130 (m-30) REVERT: A 608 LEU cc_start: 0.7416 (mt) cc_final: 0.7174 (mt) REVERT: A 637 GLN cc_start: 0.5700 (mp10) cc_final: 0.5143 (mp-120) REVERT: B 47 SER cc_start: 0.6198 (m) cc_final: 0.5746 (p) REVERT: B 93 GLU cc_start: 0.6723 (mp0) cc_final: 0.6357 (mt-10) REVERT: B 96 MET cc_start: 0.5230 (mtm) cc_final: 0.4907 (mtm) REVERT: B 139 ARG cc_start: 0.6899 (mtt-85) cc_final: 0.6494 (mpt180) REVERT: B 177 GLU cc_start: 0.7101 (mp0) cc_final: 0.6683 (mp0) REVERT: B 263 ARG cc_start: 0.7611 (mtt-85) cc_final: 0.7323 (mtm-85) REVERT: B 311 THR cc_start: 0.6097 (OUTLIER) cc_final: 0.5236 (m) REVERT: B 379 THR cc_start: 0.7899 (t) cc_final: 0.7673 (p) REVERT: B 381 LYS cc_start: 0.7994 (mtmt) cc_final: 0.7746 (mtpt) REVERT: B 392 THR cc_start: 0.8465 (t) cc_final: 0.8205 (m) REVERT: B 458 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8414 (mt) REVERT: B 497 MET cc_start: 0.8172 (mtt) cc_final: 0.7936 (mtm) REVERT: B 524 TYR cc_start: 0.8037 (p90) cc_final: 0.7793 (p90) REVERT: B 535 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7336 (mt-10) REVERT: B 590 ASP cc_start: 0.7573 (m-30) cc_final: 0.7309 (m-30) REVERT: B 637 GLN cc_start: 0.6030 (mp10) cc_final: 0.5400 (mp-120) REVERT: C 78 MET cc_start: 0.7261 (mmt) cc_final: 0.6949 (mmp) REVERT: C 93 GLU cc_start: 0.6660 (mp0) cc_final: 0.6296 (mt-10) REVERT: C 96 MET cc_start: 0.5037 (mtm) cc_final: 0.4706 (mtm) REVERT: C 139 ARG cc_start: 0.6683 (mtt-85) cc_final: 0.6321 (mtm180) REVERT: C 177 GLU cc_start: 0.7106 (mp0) cc_final: 0.6614 (mp0) REVERT: C 263 ARG cc_start: 0.7597 (mtt-85) cc_final: 0.7281 (mtm-85) REVERT: C 311 THR cc_start: 0.6077 (OUTLIER) cc_final: 0.5111 (m) REVERT: C 375 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7555 (mt-10) REVERT: C 379 THR cc_start: 0.7870 (t) cc_final: 0.7530 (p) REVERT: C 381 LYS cc_start: 0.7866 (mtmt) cc_final: 0.7596 (mtpt) REVERT: C 392 THR cc_start: 0.8431 (t) cc_final: 0.8204 (m) REVERT: C 458 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8406 (mt) REVERT: C 497 MET cc_start: 0.8073 (mtt) cc_final: 0.7808 (mtm) REVERT: C 524 TYR cc_start: 0.7991 (p90) cc_final: 0.7682 (p90) REVERT: C 535 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7441 (mt-10) REVERT: C 589 ARG cc_start: 0.7232 (tmm160) cc_final: 0.6930 (ttm-80) REVERT: C 590 ASP cc_start: 0.7567 (m-30) cc_final: 0.7296 (m-30) REVERT: C 637 GLN cc_start: 0.5940 (mp10) cc_final: 0.5294 (mp-120) REVERT: D 78 MET cc_start: 0.7306 (mmt) cc_final: 0.6987 (mmp) REVERT: D 93 GLU cc_start: 0.6671 (mp0) cc_final: 0.6297 (mt-10) REVERT: D 96 MET cc_start: 0.5035 (mtm) cc_final: 0.4663 (mtm) REVERT: D 139 ARG cc_start: 0.6702 (mtt-85) cc_final: 0.6309 (mtm180) REVERT: D 177 GLU cc_start: 0.7101 (mp0) cc_final: 0.6590 (mp0) REVERT: D 263 ARG cc_start: 0.7642 (mtt-85) cc_final: 0.7197 (mtm-85) REVERT: D 311 THR cc_start: 0.6051 (OUTLIER) cc_final: 0.5117 (m) REVERT: D 375 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7534 (mt-10) REVERT: D 379 THR cc_start: 0.7801 (t) cc_final: 0.7373 (p) REVERT: D 381 LYS cc_start: 0.7896 (mtmt) cc_final: 0.7610 (mtpt) REVERT: D 392 THR cc_start: 0.8456 (t) cc_final: 0.8222 (m) REVERT: D 458 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8390 (mt) REVERT: D 497 MET cc_start: 0.8075 (mtt) cc_final: 0.7817 (mtm) REVERT: D 535 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7475 (mt-10) REVERT: D 589 ARG cc_start: 0.7207 (tmm160) cc_final: 0.6879 (ttm-80) REVERT: D 590 ASP cc_start: 0.7538 (m-30) cc_final: 0.7243 (m-30) REVERT: D 608 LEU cc_start: 0.7376 (mt) cc_final: 0.7175 (mt) REVERT: D 637 GLN cc_start: 0.5748 (mp10) cc_final: 0.5201 (mp-120) outliers start: 32 outliers final: 5 residues processed: 528 average time/residue: 0.5474 time to fit residues: 328.8818 Evaluate side-chains 378 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 366 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 20.0000 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 235 optimal weight: 0.5980 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 ASN A 118 GLN A 122 HIS A 174 ASN A 225 HIS A 369 GLN A 370 GLN A 546 ASN A 572 ASN B 37 ASN B 118 GLN B 122 HIS B 174 ASN B 225 HIS B 369 GLN B 370 GLN B 546 ASN B 572 ASN B 582 HIS C 37 ASN C 118 GLN C 122 HIS C 174 ASN C 225 HIS C 369 GLN C 370 GLN C 546 ASN C 572 ASN D 37 ASN D 118 GLN D 122 HIS D 174 ASN D 225 HIS D 369 GLN D 370 GLN D 546 ASN D 572 ASN D 582 HIS Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.195705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.129742 restraints weight = 20927.546| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.83 r_work: 0.3217 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3025 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 21920 Z= 0.223 Angle : 0.716 8.078 29436 Z= 0.358 Chirality : 0.045 0.290 3204 Planarity : 0.006 0.049 3552 Dihedral : 19.217 179.721 4720 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.98 % Allowed : 7.47 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.65 (0.15), residues: 2432 helix: -1.60 (0.11), residues: 1460 sheet: -2.19 (0.66), residues: 76 loop : -1.71 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 146 TYR 0.021 0.003 TYR D 377 PHE 0.023 0.002 PHE A 537 TRP 0.014 0.002 TRP D 613 HIS 0.007 0.002 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.22 (21920) covalent geometry : angle 0.71628 / 0.36 (29436) hydrogen bonds : bond 0.06781 / 4.47 ( 1010) hydrogen bonds : angle 4.63515 / 3.17 ( 2922) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 396 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.6423 (OUTLIER) cc_final: 0.6063 (tm) REVERT: A 96 MET cc_start: 0.5427 (mtm) cc_final: 0.5138 (mtm) REVERT: A 177 GLU cc_start: 0.7157 (mp0) cc_final: 0.6823 (mp0) REVERT: A 375 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7927 (mt-10) REVERT: A 378 MET cc_start: 0.8360 (mtt) cc_final: 0.7957 (mtp) REVERT: A 381 LYS cc_start: 0.7420 (mtmt) cc_final: 0.7190 (mtpt) REVERT: A 458 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8541 (mt) REVERT: A 535 GLU cc_start: 0.8342 (mt-10) cc_final: 0.7706 (mt-10) REVERT: A 608 LEU cc_start: 0.7774 (mt) cc_final: 0.7471 (mt) REVERT: A 610 ARG cc_start: 0.6642 (tpp-160) cc_final: 0.6356 (tpt170) REVERT: A 618 ILE cc_start: 0.7959 (OUTLIER) cc_final: 0.7672 (mt) REVERT: A 637 GLN cc_start: 0.6252 (mp10) cc_final: 0.5993 (mp-120) REVERT: B 51 LEU cc_start: 0.6276 (OUTLIER) cc_final: 0.5925 (tm) REVERT: B 80 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7692 (pt0) REVERT: B 93 GLU cc_start: 0.7025 (mp0) cc_final: 0.6655 (mp0) REVERT: B 96 MET cc_start: 0.5279 (mtm) cc_final: 0.4984 (mtm) REVERT: B 177 GLU cc_start: 0.7150 (mp0) cc_final: 0.6771 (mp0) REVERT: B 381 LYS cc_start: 0.7352 (mtmt) cc_final: 0.7091 (mtpt) REVERT: B 392 THR cc_start: 0.8334 (t) cc_final: 0.7983 (m) REVERT: B 535 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7857 (mt-10) REVERT: B 590 ASP cc_start: 0.7945 (m-30) cc_final: 0.7713 (m-30) REVERT: B 610 ARG cc_start: 0.6671 (tpm170) cc_final: 0.6330 (tpt170) REVERT: B 618 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7609 (mt) REVERT: B 637 GLN cc_start: 0.6197 (mp10) cc_final: 0.5948 (mp-120) REVERT: C 78 MET cc_start: 0.7612 (mmt) cc_final: 0.7187 (mmp) REVERT: C 93 GLU cc_start: 0.7024 (mp0) cc_final: 0.6630 (mp0) REVERT: C 96 MET cc_start: 0.5390 (mtm) cc_final: 0.5099 (mtm) REVERT: C 177 GLU cc_start: 0.7140 (mp0) cc_final: 0.6794 (mp0) REVERT: C 375 GLU cc_start: 0.8217 (mt-10) cc_final: 0.8014 (mt-10) REVERT: C 381 LYS cc_start: 0.7388 (mtmt) cc_final: 0.7132 (mtpt) REVERT: C 392 THR cc_start: 0.8355 (t) cc_final: 0.8009 (m) REVERT: C 535 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7648 (mt-10) REVERT: C 610 ARG cc_start: 0.6691 (tpm170) cc_final: 0.6391 (tpt170) REVERT: C 618 ILE cc_start: 0.7914 (OUTLIER) cc_final: 0.7617 (mt) REVERT: C 637 GLN cc_start: 0.6162 (mp10) cc_final: 0.5873 (mp-120) REVERT: D 78 MET cc_start: 0.7657 (mmt) cc_final: 0.7261 (mmp) REVERT: D 80 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7711 (pt0) REVERT: D 93 GLU cc_start: 0.7063 (mp0) cc_final: 0.6669 (mp0) REVERT: D 96 MET cc_start: 0.5315 (mtm) cc_final: 0.4942 (mtm) REVERT: D 177 GLU cc_start: 0.7133 (mp0) cc_final: 0.6780 (mp0) REVERT: D 375 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7914 (mt-10) REVERT: D 381 LYS cc_start: 0.7396 (mtmt) cc_final: 0.7075 (mtpt) REVERT: D 392 THR cc_start: 0.8356 (t) cc_final: 0.8010 (m) REVERT: D 535 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7882 (mt-10) REVERT: D 608 LEU cc_start: 0.7743 (mt) cc_final: 0.7461 (mt) REVERT: D 610 ARG cc_start: 0.6662 (tpm170) cc_final: 0.6398 (tpm170) REVERT: D 618 ILE cc_start: 0.7937 (OUTLIER) cc_final: 0.7642 (mt) REVERT: D 637 GLN cc_start: 0.6219 (mp10) cc_final: 0.5978 (mp-120) outliers start: 63 outliers final: 23 residues processed: 438 average time/residue: 0.5427 time to fit residues: 270.4764 Evaluate side-chains 387 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 355 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 97 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 157 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 148 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 ASN A 174 ASN A 197 ASN A 582 HIS B 37 ASN B 197 ASN C 37 ASN C 197 ASN C 582 HIS D 37 ASN D 174 ASN D 197 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.199366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.136015 restraints weight = 20809.448| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.00 r_work: 0.3293 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 21920 Z= 0.112 Angle : 0.547 7.852 29436 Z= 0.277 Chirality : 0.039 0.203 3204 Planarity : 0.005 0.039 3552 Dihedral : 17.358 156.720 4718 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.50 % Allowed : 10.78 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.17), residues: 2432 helix: -0.01 (0.13), residues: 1460 sheet: -1.97 (0.63), residues: 76 loop : -1.27 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 180 TYR 0.012 0.002 TYR C 467 PHE 0.012 0.001 PHE C 537 TRP 0.009 0.001 TRP C 593 HIS 0.004 0.001 HIS B 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (21920) covalent geometry : angle 0.54709 / 0.28 (29436) hydrogen bonds : bond 0.04628 / 3.06 ( 1010) hydrogen bonds : angle 4.03810 / 2.76 ( 2922) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 384 time to evaluate : 0.732 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.6350 (OUTLIER) cc_final: 0.6008 (tm) REVERT: A 93 GLU cc_start: 0.7275 (mp0) cc_final: 0.6476 (mp0) REVERT: A 96 MET cc_start: 0.5419 (mtm) cc_final: 0.5055 (mtm) REVERT: A 131 ASN cc_start: 0.6872 (OUTLIER) cc_final: 0.6315 (m-40) REVERT: A 177 GLU cc_start: 0.7136 (mp0) cc_final: 0.6865 (mp0) REVERT: A 311 THR cc_start: 0.5292 (OUTLIER) cc_final: 0.4654 (p) REVERT: A 375 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7935 (mt-10) REVERT: A 378 MET cc_start: 0.8367 (mtt) cc_final: 0.8033 (mtm) REVERT: A 535 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7572 (mt-10) REVERT: A 591 GLU cc_start: 0.7941 (pt0) cc_final: 0.7493 (mp0) REVERT: A 608 LEU cc_start: 0.7693 (mt) cc_final: 0.7406 (mt) REVERT: A 618 ILE cc_start: 0.7926 (OUTLIER) cc_final: 0.7636 (mt) REVERT: A 637 GLN cc_start: 0.6255 (mp10) cc_final: 0.5938 (mp-120) REVERT: B 51 LEU cc_start: 0.6286 (OUTLIER) cc_final: 0.5940 (tm) REVERT: B 93 GLU cc_start: 0.6994 (mp0) cc_final: 0.6671 (mp0) REVERT: B 96 MET cc_start: 0.5371 (mtm) cc_final: 0.4987 (mtm) REVERT: B 131 ASN cc_start: 0.6851 (OUTLIER) cc_final: 0.6310 (m-40) REVERT: B 177 GLU cc_start: 0.7123 (mp0) cc_final: 0.6829 (mp0) REVERT: B 311 THR cc_start: 0.5427 (OUTLIER) cc_final: 0.4866 (p) REVERT: B 458 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8592 (mt) REVERT: B 535 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7685 (mt-10) REVERT: B 590 ASP cc_start: 0.7870 (m-30) cc_final: 0.7658 (m-30) REVERT: B 591 GLU cc_start: 0.7948 (pt0) cc_final: 0.7504 (mp0) REVERT: B 610 ARG cc_start: 0.6501 (tpm170) cc_final: 0.6297 (tpt170) REVERT: B 618 ILE cc_start: 0.7845 (OUTLIER) cc_final: 0.7572 (mt) REVERT: B 637 GLN cc_start: 0.6207 (mp10) cc_final: 0.5900 (mp-120) REVERT: C 93 GLU cc_start: 0.6991 (mp0) cc_final: 0.6663 (mp0) REVERT: C 96 MET cc_start: 0.5446 (mtm) cc_final: 0.5035 (mtm) REVERT: C 131 ASN cc_start: 0.6852 (OUTLIER) cc_final: 0.6296 (m-40) REVERT: C 177 GLU cc_start: 0.7088 (mp0) cc_final: 0.6814 (mp0) REVERT: C 311 THR cc_start: 0.5290 (OUTLIER) cc_final: 0.4672 (p) REVERT: C 375 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7953 (mt-10) REVERT: C 458 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8583 (mt) REVERT: C 535 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7587 (mt-10) REVERT: C 610 ARG cc_start: 0.6519 (tpm170) cc_final: 0.6309 (tpt170) REVERT: C 618 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7614 (mt) REVERT: D 93 GLU cc_start: 0.7006 (mp0) cc_final: 0.6680 (mp0) REVERT: D 96 MET cc_start: 0.5380 (mtm) cc_final: 0.4953 (mtm) REVERT: D 131 ASN cc_start: 0.6869 (OUTLIER) cc_final: 0.6313 (m-40) REVERT: D 177 GLU cc_start: 0.7075 (mp0) cc_final: 0.6788 (mp0) REVERT: D 311 THR cc_start: 0.5348 (OUTLIER) cc_final: 0.4717 (p) REVERT: D 375 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7867 (mt-10) REVERT: D 458 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8599 (mt) REVERT: D 535 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7677 (mt-10) REVERT: D 591 GLU cc_start: 0.7926 (pt0) cc_final: 0.7473 (mp0) REVERT: D 608 LEU cc_start: 0.7656 (mt) cc_final: 0.7351 (mt) REVERT: D 610 ARG cc_start: 0.6542 (tpm170) cc_final: 0.6314 (tpt170) REVERT: D 618 ILE cc_start: 0.7885 (OUTLIER) cc_final: 0.7598 (mt) REVERT: D 637 GLN cc_start: 0.6195 (mp10) cc_final: 0.5881 (mp-120) outliers start: 53 outliers final: 12 residues processed: 425 average time/residue: 0.5711 time to fit residues: 280.0059 Evaluate side-chains 372 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 343 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 131 ASN Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 14 optimal weight: 0.5980 chunk 155 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 218 optimal weight: 0.8980 chunk 157 optimal weight: 0.6980 chunk 110 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 200 optimal weight: 0.9980 chunk 210 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 185 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.200039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.137857 restraints weight = 20865.914| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.04 r_work: 0.3288 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 21920 Z= 0.108 Angle : 0.530 7.527 29436 Z= 0.267 Chirality : 0.039 0.145 3204 Planarity : 0.004 0.039 3552 Dihedral : 16.137 140.434 4718 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.36 % Allowed : 13.14 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.17), residues: 2432 helix: 0.68 (0.14), residues: 1456 sheet: -1.54 (0.64), residues: 76 loop : -1.06 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 180 TYR 0.011 0.001 TYR B 467 PHE 0.013 0.001 PHE C 408 TRP 0.008 0.001 TRP C 593 HIS 0.005 0.001 HIS D 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (21920) covalent geometry : angle 0.53011 / 0.27 (29436) hydrogen bonds : bond 0.04278 / 2.84 ( 1010) hydrogen bonds : angle 3.85972 / 2.64 ( 2922) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 370 time to evaluate : 0.830 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.6297 (OUTLIER) cc_final: 0.5943 (tm) REVERT: A 93 GLU cc_start: 0.7257 (mp0) cc_final: 0.6464 (mp0) REVERT: A 96 MET cc_start: 0.5404 (mtm) cc_final: 0.4988 (mtm) REVERT: A 131 ASN cc_start: 0.6807 (m110) cc_final: 0.6272 (m-40) REVERT: A 177 GLU cc_start: 0.7130 (mp0) cc_final: 0.6800 (pm20) REVERT: A 311 THR cc_start: 0.5337 (OUTLIER) cc_final: 0.4721 (p) REVERT: A 375 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7934 (mt-10) REVERT: A 379 THR cc_start: 0.7160 (OUTLIER) cc_final: 0.6918 (p) REVERT: A 535 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7703 (mt-10) REVERT: A 591 GLU cc_start: 0.7887 (pt0) cc_final: 0.7466 (mp0) REVERT: A 608 LEU cc_start: 0.7599 (mt) cc_final: 0.7315 (mt) REVERT: A 618 ILE cc_start: 0.7919 (OUTLIER) cc_final: 0.7615 (mt) REVERT: A 637 GLN cc_start: 0.6252 (mp10) cc_final: 0.5982 (mp-120) REVERT: B 51 LEU cc_start: 0.6315 (OUTLIER) cc_final: 0.5965 (tm) REVERT: B 93 GLU cc_start: 0.6880 (mp0) cc_final: 0.6548 (mp0) REVERT: B 96 MET cc_start: 0.5358 (mtm) cc_final: 0.4935 (mtm) REVERT: B 131 ASN cc_start: 0.6803 (OUTLIER) cc_final: 0.6312 (m-40) REVERT: B 177 GLU cc_start: 0.7090 (mp0) cc_final: 0.6800 (mp0) REVERT: B 311 THR cc_start: 0.5484 (OUTLIER) cc_final: 0.4959 (p) REVERT: B 458 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8581 (mt) REVERT: B 535 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7612 (mt-10) REVERT: B 590 ASP cc_start: 0.7859 (m-30) cc_final: 0.7654 (m-30) REVERT: B 591 GLU cc_start: 0.7924 (pt0) cc_final: 0.7477 (mp0) REVERT: B 610 ARG cc_start: 0.6491 (tpm170) cc_final: 0.6169 (tpt170) REVERT: B 618 ILE cc_start: 0.7818 (OUTLIER) cc_final: 0.7531 (mt) REVERT: B 637 GLN cc_start: 0.6338 (mp10) cc_final: 0.6097 (mp-120) REVERT: C 93 GLU cc_start: 0.6884 (mp0) cc_final: 0.6538 (mp0) REVERT: C 96 MET cc_start: 0.5406 (mtm) cc_final: 0.5002 (mtm) REVERT: C 131 ASN cc_start: 0.6805 (OUTLIER) cc_final: 0.6284 (m-40) REVERT: C 177 GLU cc_start: 0.6987 (mp0) cc_final: 0.6722 (mp0) REVERT: C 311 THR cc_start: 0.5439 (OUTLIER) cc_final: 0.4829 (p) REVERT: C 458 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8573 (mt) REVERT: C 535 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7640 (mt-10) REVERT: C 591 GLU cc_start: 0.7912 (pt0) cc_final: 0.7497 (mp0) REVERT: C 610 ARG cc_start: 0.6473 (tpm170) cc_final: 0.6227 (tpm170) REVERT: C 618 ILE cc_start: 0.7865 (OUTLIER) cc_final: 0.7576 (mt) REVERT: D 93 GLU cc_start: 0.6962 (mp0) cc_final: 0.6617 (mp0) REVERT: D 96 MET cc_start: 0.5496 (mtm) cc_final: 0.5026 (mtm) REVERT: D 131 ASN cc_start: 0.6793 (m110) cc_final: 0.6280 (m-40) REVERT: D 177 GLU cc_start: 0.7074 (mp0) cc_final: 0.6792 (mp0) REVERT: D 311 THR cc_start: 0.5447 (OUTLIER) cc_final: 0.4846 (p) REVERT: D 458 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8575 (mt) REVERT: D 535 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7701 (mt-10) REVERT: D 591 GLU cc_start: 0.7883 (pt0) cc_final: 0.7464 (mp0) REVERT: D 608 LEU cc_start: 0.7576 (mt) cc_final: 0.7263 (mt) REVERT: D 610 ARG cc_start: 0.6324 (tpm170) cc_final: 0.6011 (tpt170) REVERT: D 618 ILE cc_start: 0.7858 (OUTLIER) cc_final: 0.7580 (mt) REVERT: D 637 GLN cc_start: 0.6310 (mp10) cc_final: 0.6016 (mp-120) outliers start: 50 outliers final: 11 residues processed: 411 average time/residue: 0.6116 time to fit residues: 288.1136 Evaluate side-chains 374 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 347 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 131 ASN Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 194 optimal weight: 20.0000 chunk 180 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 243 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 chunk 153 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 141 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 185 HIS D 91 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.194790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.129385 restraints weight = 20775.876| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.85 r_work: 0.3226 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3054 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3054 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 21920 Z= 0.192 Angle : 0.624 7.760 29436 Z= 0.309 Chirality : 0.044 0.207 3204 Planarity : 0.005 0.050 3552 Dihedral : 16.336 153.184 4718 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.22 % Allowed : 13.33 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.17), residues: 2432 helix: 0.81 (0.14), residues: 1464 sheet: -1.37 (0.64), residues: 76 loop : -1.08 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 146 TYR 0.014 0.002 TYR A 377 PHE 0.015 0.002 PHE D 537 TRP 0.008 0.001 TRP A 495 HIS 0.005 0.001 HIS B 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.19 (21920) covalent geometry : angle 0.62433 / 0.31 (29436) hydrogen bonds : bond 0.05430 / 3.59 ( 1010) hydrogen bonds : angle 3.99766 / 2.74 ( 2922) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 349 time to evaluate : 0.753 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.6321 (OUTLIER) cc_final: 0.5948 (tm) REVERT: A 93 GLU cc_start: 0.7263 (mp0) cc_final: 0.6502 (mp0) REVERT: A 96 MET cc_start: 0.5313 (mtm) cc_final: 0.4937 (mtm) REVERT: A 131 ASN cc_start: 0.6826 (m110) cc_final: 0.6284 (m-40) REVERT: A 177 GLU cc_start: 0.7128 (mp0) cc_final: 0.6803 (pm20) REVERT: A 491 MET cc_start: 0.8263 (mmp) cc_final: 0.7969 (mmp) REVERT: A 588 GLU cc_start: 0.8104 (pt0) cc_final: 0.7823 (pt0) REVERT: A 608 LEU cc_start: 0.7543 (mt) cc_final: 0.7306 (mt) REVERT: A 618 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7674 (mt) REVERT: A 637 GLN cc_start: 0.6370 (mp10) cc_final: 0.6133 (mp-120) REVERT: B 51 LEU cc_start: 0.6275 (OUTLIER) cc_final: 0.5920 (tm) REVERT: B 93 GLU cc_start: 0.6897 (mp0) cc_final: 0.6530 (mp0) REVERT: B 96 MET cc_start: 0.5398 (mtm) cc_final: 0.4963 (mtm) REVERT: B 131 ASN cc_start: 0.6837 (m110) cc_final: 0.6326 (m-40) REVERT: B 146 ARG cc_start: 0.7466 (mtp-110) cc_final: 0.7243 (mtp-110) REVERT: B 177 GLU cc_start: 0.7118 (mp0) cc_final: 0.6810 (mp0) REVERT: B 588 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7838 (pt0) REVERT: B 590 ASP cc_start: 0.7929 (m-30) cc_final: 0.7720 (m-30) REVERT: B 637 GLN cc_start: 0.6423 (mp10) cc_final: 0.6184 (mp-120) REVERT: C 93 GLU cc_start: 0.6958 (mp0) cc_final: 0.6602 (mp0) REVERT: C 96 MET cc_start: 0.5359 (mtm) cc_final: 0.4943 (mtm) REVERT: C 131 ASN cc_start: 0.6843 (m110) cc_final: 0.6303 (m-40) REVERT: C 146 ARG cc_start: 0.7460 (mtp-110) cc_final: 0.7238 (mtp-110) REVERT: C 177 GLU cc_start: 0.7126 (mp0) cc_final: 0.6792 (mp0) REVERT: C 588 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7816 (pt0) REVERT: C 618 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7644 (mt) REVERT: D 93 GLU cc_start: 0.6952 (mp0) cc_final: 0.6638 (mp0) REVERT: D 96 MET cc_start: 0.5524 (mtm) cc_final: 0.5114 (mtm) REVERT: D 131 ASN cc_start: 0.6807 (m110) cc_final: 0.6273 (m-40) REVERT: D 177 GLU cc_start: 0.7130 (mp0) cc_final: 0.6796 (mp0) REVERT: D 378 MET cc_start: 0.8296 (mtm) cc_final: 0.8087 (mtp) REVERT: D 608 LEU cc_start: 0.7533 (mt) cc_final: 0.7304 (mt) REVERT: D 610 ARG cc_start: 0.6424 (tpm170) cc_final: 0.6159 (tpt170) REVERT: D 618 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7664 (mt) REVERT: D 637 GLN cc_start: 0.6427 (mp10) cc_final: 0.6171 (mp-120) outliers start: 47 outliers final: 24 residues processed: 384 average time/residue: 0.5505 time to fit residues: 245.1445 Evaluate side-chains 368 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 337 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 588 GLU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 588 GLU Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 80 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 122 optimal weight: 9.9990 chunk 227 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 39 optimal weight: 0.1980 chunk 154 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.197937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.132590 restraints weight = 20538.609| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.95 r_work: 0.3269 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3087 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3087 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21920 Z= 0.129 Angle : 0.550 7.250 29436 Z= 0.275 Chirality : 0.040 0.176 3204 Planarity : 0.004 0.052 3552 Dihedral : 15.434 146.015 4715 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.89 % Allowed : 14.56 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.17), residues: 2432 helix: 1.05 (0.14), residues: 1464 sheet: -1.20 (0.64), residues: 76 loop : -0.95 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 146 TYR 0.012 0.002 TYR C 467 PHE 0.010 0.001 PHE B 537 TRP 0.007 0.001 TRP C 593 HIS 0.003 0.001 HIS B 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (21920) covalent geometry : angle 0.54954 / 0.27 (29436) hydrogen bonds : bond 0.04604 / 3.04 ( 1010) hydrogen bonds : angle 3.84091 / 2.63 ( 2922) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 358 time to evaluate : 0.885 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.6381 (OUTLIER) cc_final: 0.6026 (tm) REVERT: A 93 GLU cc_start: 0.7263 (mp0) cc_final: 0.6486 (mp0) REVERT: A 96 MET cc_start: 0.5329 (mtm) cc_final: 0.4927 (mtm) REVERT: A 131 ASN cc_start: 0.6839 (m110) cc_final: 0.6333 (m-40) REVERT: A 177 GLU cc_start: 0.7126 (mp0) cc_final: 0.6798 (pm20) REVERT: A 379 THR cc_start: 0.7159 (OUTLIER) cc_final: 0.6923 (p) REVERT: A 535 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7663 (mt-10) REVERT: A 588 GLU cc_start: 0.8073 (pt0) cc_final: 0.7818 (pt0) REVERT: A 591 GLU cc_start: 0.7960 (pt0) cc_final: 0.7488 (mp0) REVERT: A 608 LEU cc_start: 0.7551 (mt) cc_final: 0.7295 (mt) REVERT: A 610 ARG cc_start: 0.6522 (tpm170) cc_final: 0.6293 (tpm170) REVERT: A 618 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7697 (mt) REVERT: B 51 LEU cc_start: 0.6376 (OUTLIER) cc_final: 0.6031 (tm) REVERT: B 85 ILE cc_start: 0.7126 (mp) cc_final: 0.6893 (mp) REVERT: B 93 GLU cc_start: 0.6951 (mp0) cc_final: 0.6587 (mp0) REVERT: B 96 MET cc_start: 0.5347 (mtm) cc_final: 0.4919 (mtm) REVERT: B 131 ASN cc_start: 0.6830 (m110) cc_final: 0.6321 (m-40) REVERT: B 146 ARG cc_start: 0.7410 (mtp-110) cc_final: 0.7160 (mtp-110) REVERT: B 177 GLU cc_start: 0.7122 (mp0) cc_final: 0.6814 (mp0) REVERT: B 491 MET cc_start: 0.8301 (mmp) cc_final: 0.8037 (mmp) REVERT: B 535 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7743 (mt-10) REVERT: B 590 ASP cc_start: 0.7917 (m-30) cc_final: 0.7708 (m-30) REVERT: B 618 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7549 (mt) REVERT: C 96 MET cc_start: 0.5282 (mtm) cc_final: 0.4892 (mtm) REVERT: C 131 ASN cc_start: 0.6837 (m110) cc_final: 0.6303 (m-40) REVERT: C 146 ARG cc_start: 0.7450 (mtp-110) cc_final: 0.7211 (mtp-110) REVERT: C 177 GLU cc_start: 0.7115 (mp0) cc_final: 0.6751 (mp0) REVERT: C 491 MET cc_start: 0.8334 (mmp) cc_final: 0.8069 (mmp) REVERT: C 535 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7748 (mt-10) REVERT: C 588 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7887 (pt0) REVERT: C 591 GLU cc_start: 0.7971 (pt0) cc_final: 0.7500 (mp0) REVERT: C 618 ILE cc_start: 0.7992 (OUTLIER) cc_final: 0.7668 (mt) REVERT: D 93 GLU cc_start: 0.6976 (mp0) cc_final: 0.6662 (mp0) REVERT: D 96 MET cc_start: 0.5622 (mtm) cc_final: 0.5198 (mtm) REVERT: D 131 ASN cc_start: 0.6837 (m110) cc_final: 0.6312 (m-40) REVERT: D 177 GLU cc_start: 0.7140 (mp0) cc_final: 0.6779 (mp0) REVERT: D 491 MET cc_start: 0.8336 (mmp) cc_final: 0.8100 (mmp) REVERT: D 535 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7756 (mt-10) REVERT: D 591 GLU cc_start: 0.7944 (pt0) cc_final: 0.7495 (mp0) REVERT: D 608 LEU cc_start: 0.7599 (mt) cc_final: 0.7347 (mt) REVERT: D 610 ARG cc_start: 0.6411 (tpm170) cc_final: 0.6108 (tpt170) outliers start: 40 outliers final: 17 residues processed: 390 average time/residue: 0.5268 time to fit residues: 237.9305 Evaluate side-chains 365 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 341 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 588 GLU Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 237 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 177 optimal weight: 5.9990 chunk 186 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 ASN A 201 HIS ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS C 201 HIS D 91 ASN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.193204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.126912 restraints weight = 20401.132| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.90 r_work: 0.3183 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 21920 Z= 0.272 Angle : 0.712 8.765 29436 Z= 0.348 Chirality : 0.048 0.263 3204 Planarity : 0.005 0.044 3552 Dihedral : 16.603 156.795 4714 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.60 % Allowed : 14.79 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.17), residues: 2432 helix: 0.78 (0.14), residues: 1464 sheet: -1.64 (0.57), residues: 84 loop : -0.96 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 146 TYR 0.017 0.003 TYR D 377 PHE 0.015 0.002 PHE C 537 TRP 0.008 0.002 TRP A 495 HIS 0.006 0.002 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00686 / 0.27 (21920) covalent geometry : angle 0.71154 / 0.35 (29436) hydrogen bonds : bond 0.06165 / 4.07 ( 1010) hydrogen bonds : angle 4.08590 / 2.80 ( 2922) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 342 time to evaluate : 0.735 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.6479 (OUTLIER) cc_final: 0.6122 (tm) REVERT: A 93 GLU cc_start: 0.7179 (mp0) cc_final: 0.6453 (mp0) REVERT: A 96 MET cc_start: 0.5329 (mtm) cc_final: 0.4960 (mtm) REVERT: A 131 ASN cc_start: 0.6834 (m110) cc_final: 0.6276 (m-40) REVERT: A 177 GLU cc_start: 0.7162 (mp0) cc_final: 0.6899 (mp0) REVERT: A 491 MET cc_start: 0.8384 (mmp) cc_final: 0.8158 (mmp) REVERT: A 608 LEU cc_start: 0.7661 (mt) cc_final: 0.7459 (mt) REVERT: A 610 ARG cc_start: 0.6539 (tpt170) cc_final: 0.6275 (tpt170) REVERT: B 51 LEU cc_start: 0.6466 (OUTLIER) cc_final: 0.6120 (tm) REVERT: B 93 GLU cc_start: 0.7056 (mp0) cc_final: 0.6653 (mp0) REVERT: B 96 MET cc_start: 0.5378 (mtm) cc_final: 0.4953 (mtm) REVERT: B 131 ASN cc_start: 0.6844 (m110) cc_final: 0.6304 (m-40) REVERT: B 177 GLU cc_start: 0.7113 (mp0) cc_final: 0.6770 (mp0) REVERT: B 190 ARG cc_start: 0.7055 (OUTLIER) cc_final: 0.6820 (mtp-110) REVERT: B 588 GLU cc_start: 0.8208 (pt0) cc_final: 0.7973 (pt0) REVERT: B 590 ASP cc_start: 0.8036 (m-30) cc_final: 0.7833 (m-30) REVERT: B 618 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7668 (mt) REVERT: C 93 GLU cc_start: 0.7210 (mp0) cc_final: 0.6452 (mp0) REVERT: C 96 MET cc_start: 0.5421 (mtm) cc_final: 0.5028 (mtm) REVERT: C 131 ASN cc_start: 0.6878 (m110) cc_final: 0.6278 (m-40) REVERT: C 177 GLU cc_start: 0.7028 (mp0) cc_final: 0.6596 (mp0) REVERT: C 588 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7937 (pt0) REVERT: D 93 GLU cc_start: 0.6948 (mp0) cc_final: 0.6578 (mp0) REVERT: D 96 MET cc_start: 0.5645 (mtm) cc_final: 0.5231 (mtm) REVERT: D 131 ASN cc_start: 0.6825 (m110) cc_final: 0.6270 (m-40) REVERT: D 177 GLU cc_start: 0.7083 (mp0) cc_final: 0.6708 (mp0) REVERT: D 588 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7905 (pt0) REVERT: D 610 ARG cc_start: 0.6405 (tpm170) cc_final: 0.6154 (mmt180) REVERT: D 618 ILE cc_start: 0.8102 (OUTLIER) cc_final: 0.7701 (mt) outliers start: 55 outliers final: 24 residues processed: 381 average time/residue: 0.4982 time to fit residues: 221.3273 Evaluate side-chains 369 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 338 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 588 GLU Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 588 GLU Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 171 optimal weight: 0.2980 chunk 126 optimal weight: 0.0470 chunk 162 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 228 optimal weight: 0.9990 chunk 174 optimal weight: 0.9990 chunk 187 optimal weight: 0.0770 chunk 141 optimal weight: 8.9990 chunk 190 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.4840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 GLN B 91 ASN B 118 GLN C 91 ASN C 637 GLN D 118 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.200536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.136542 restraints weight = 20419.780| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.00 r_work: 0.3299 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 21920 Z= 0.100 Angle : 0.520 8.004 29436 Z= 0.261 Chirality : 0.039 0.141 3204 Planarity : 0.004 0.041 3552 Dihedral : 14.813 136.581 4714 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.13 % Allowed : 15.64 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.17), residues: 2432 helix: 1.23 (0.14), residues: 1452 sheet: -1.13 (0.60), residues: 80 loop : -0.69 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 180 TYR 0.012 0.001 TYR B 467 PHE 0.010 0.001 PHE C 493 TRP 0.008 0.001 TRP D 593 HIS 0.003 0.001 HIS D 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 (21920) covalent geometry : angle 0.52024 / 0.26 (29436) hydrogen bonds : bond 0.04031 / 2.67 ( 1010) hydrogen bonds : angle 3.76345 / 2.57 ( 2922) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 364 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.6545 (OUTLIER) cc_final: 0.6208 (tm) REVERT: A 93 GLU cc_start: 0.7260 (mp0) cc_final: 0.6509 (mp0) REVERT: A 96 MET cc_start: 0.5414 (mtm) cc_final: 0.5049 (mtm) REVERT: A 110 MET cc_start: 0.7122 (mtt) cc_final: 0.6835 (mtt) REVERT: A 131 ASN cc_start: 0.6823 (m110) cc_final: 0.6353 (m-40) REVERT: A 177 GLU cc_start: 0.7100 (mp0) cc_final: 0.6780 (pm20) REVERT: A 379 THR cc_start: 0.7108 (OUTLIER) cc_final: 0.6898 (p) REVERT: A 535 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7641 (mt-10) REVERT: A 588 GLU cc_start: 0.7988 (pt0) cc_final: 0.7723 (pt0) REVERT: A 591 GLU cc_start: 0.7908 (pt0) cc_final: 0.7535 (mp0) REVERT: A 608 LEU cc_start: 0.7524 (mt) cc_final: 0.7246 (mt) REVERT: A 610 ARG cc_start: 0.6369 (tpt170) cc_final: 0.6070 (tpt170) REVERT: A 612 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6613 (mp) REVERT: A 618 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7698 (mt) REVERT: A 637 GLN cc_start: 0.6313 (mp-120) cc_final: 0.6035 (mp-120) REVERT: B 51 LEU cc_start: 0.6496 (OUTLIER) cc_final: 0.6157 (tm) REVERT: B 96 MET cc_start: 0.5399 (mtm) cc_final: 0.4971 (mtm) REVERT: B 110 MET cc_start: 0.7159 (mtt) cc_final: 0.6850 (mtt) REVERT: B 131 ASN cc_start: 0.6833 (m110) cc_final: 0.6383 (m-40) REVERT: B 177 GLU cc_start: 0.7141 (mp0) cc_final: 0.6810 (mp0) REVERT: B 458 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8573 (mt) REVERT: B 535 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7711 (mt-10) REVERT: B 591 GLU cc_start: 0.7927 (pt0) cc_final: 0.7536 (mp0) REVERT: C 93 GLU cc_start: 0.7206 (mp0) cc_final: 0.6467 (mp0) REVERT: C 96 MET cc_start: 0.5420 (mtm) cc_final: 0.4972 (mtm) REVERT: C 131 ASN cc_start: 0.6887 (m110) cc_final: 0.6415 (m-40) REVERT: C 177 GLU cc_start: 0.7094 (mp0) cc_final: 0.6642 (mp0) REVERT: C 458 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8571 (mt) REVERT: C 535 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7711 (mt-10) REVERT: C 588 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7773 (pt0) REVERT: C 591 GLU cc_start: 0.7913 (pt0) cc_final: 0.7533 (mp0) REVERT: C 618 ILE cc_start: 0.8067 (OUTLIER) cc_final: 0.7682 (mt) REVERT: D 93 GLU cc_start: 0.7042 (mp0) cc_final: 0.6692 (mp0) REVERT: D 96 MET cc_start: 0.5496 (mtm) cc_final: 0.5054 (mtm) REVERT: D 110 MET cc_start: 0.7169 (mtt) cc_final: 0.6856 (mtt) REVERT: D 131 ASN cc_start: 0.6789 (m110) cc_final: 0.6338 (m-40) REVERT: D 177 GLU cc_start: 0.7123 (mp0) cc_final: 0.6755 (mp0) REVERT: D 458 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8567 (mt) REVERT: D 535 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7743 (mt-10) REVERT: D 591 GLU cc_start: 0.7878 (pt0) cc_final: 0.7507 (mp0) REVERT: D 610 ARG cc_start: 0.6184 (tpm170) cc_final: 0.5829 (tpt170) outliers start: 45 outliers final: 13 residues processed: 399 average time/residue: 0.5113 time to fit residues: 236.8312 Evaluate side-chains 367 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 344 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 588 GLU Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 193 optimal weight: 0.9990 chunk 161 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 168 optimal weight: 3.9990 chunk 32 optimal weight: 0.4980 chunk 179 optimal weight: 2.9990 chunk 25 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 chunk 242 optimal weight: 20.0000 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 118 GLN B 185 HIS C 637 GLN D 91 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.198479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.133739 restraints weight = 20442.156| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.85 r_work: 0.3257 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3096 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3096 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21920 Z= 0.120 Angle : 0.544 7.603 29436 Z= 0.273 Chirality : 0.040 0.158 3204 Planarity : 0.004 0.041 3552 Dihedral : 14.630 139.302 4714 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.61 % Allowed : 16.40 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.17), residues: 2432 helix: 1.28 (0.14), residues: 1464 sheet: -0.68 (0.62), residues: 76 loop : -0.70 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 180 TYR 0.011 0.002 TYR A 328 PHE 0.011 0.001 PHE B 537 TRP 0.007 0.001 TRP D 593 HIS 0.003 0.001 HIS B 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (21920) covalent geometry : angle 0.54383 / 0.27 (29436) hydrogen bonds : bond 0.04437 / 2.93 ( 1010) hydrogen bonds : angle 3.81051 / 2.61 ( 2922) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 355 time to evaluate : 0.819 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.6553 (OUTLIER) cc_final: 0.6212 (tm) REVERT: A 93 GLU cc_start: 0.7252 (mp0) cc_final: 0.6489 (mp0) REVERT: A 96 MET cc_start: 0.5495 (mtm) cc_final: 0.5108 (mtm) REVERT: A 131 ASN cc_start: 0.6845 (m110) cc_final: 0.6401 (m-40) REVERT: A 177 GLU cc_start: 0.7129 (mp0) cc_final: 0.6805 (pm20) REVERT: A 379 THR cc_start: 0.7170 (OUTLIER) cc_final: 0.6941 (p) REVERT: A 535 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7705 (mt-10) REVERT: A 588 GLU cc_start: 0.8032 (pt0) cc_final: 0.7802 (pt0) REVERT: A 591 GLU cc_start: 0.7975 (pt0) cc_final: 0.7560 (mp0) REVERT: A 608 LEU cc_start: 0.7457 (mt) cc_final: 0.7230 (mt) REVERT: A 610 ARG cc_start: 0.6348 (tpt170) cc_final: 0.6030 (tpt170) REVERT: A 618 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7686 (mt) REVERT: B 51 LEU cc_start: 0.6529 (OUTLIER) cc_final: 0.6203 (tm) REVERT: B 93 GLU cc_start: 0.7179 (mp0) cc_final: 0.6389 (mp0) REVERT: B 96 MET cc_start: 0.5482 (mtm) cc_final: 0.5032 (mtm) REVERT: B 131 ASN cc_start: 0.6830 (m110) cc_final: 0.6408 (m-40) REVERT: B 177 GLU cc_start: 0.7112 (mp0) cc_final: 0.6786 (mp0) REVERT: B 315 GLU cc_start: 0.7892 (mp0) cc_final: 0.7641 (mp0) REVERT: B 458 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8584 (mt) REVERT: B 591 GLU cc_start: 0.7968 (pt0) cc_final: 0.7564 (mp0) REVERT: C 93 GLU cc_start: 0.7195 (mp0) cc_final: 0.6444 (mp0) REVERT: C 96 MET cc_start: 0.5481 (mtm) cc_final: 0.5033 (mtm) REVERT: C 131 ASN cc_start: 0.6842 (m110) cc_final: 0.6400 (m-40) REVERT: C 177 GLU cc_start: 0.7133 (mp0) cc_final: 0.6674 (mp0) REVERT: C 458 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8583 (mt) REVERT: C 535 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7771 (mt-10) REVERT: C 591 GLU cc_start: 0.7961 (pt0) cc_final: 0.7557 (mp0) REVERT: D 93 GLU cc_start: 0.6966 (mp0) cc_final: 0.6612 (mp0) REVERT: D 96 MET cc_start: 0.5495 (mtm) cc_final: 0.5058 (mtm) REVERT: D 131 ASN cc_start: 0.6816 (m110) cc_final: 0.6386 (m-40) REVERT: D 177 GLU cc_start: 0.7109 (mp0) cc_final: 0.6715 (mp0) REVERT: D 458 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8571 (mt) REVERT: D 535 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7814 (mt-10) REVERT: D 588 GLU cc_start: 0.8005 (pt0) cc_final: 0.7754 (pt0) REVERT: D 591 GLU cc_start: 0.7965 (pt0) cc_final: 0.7558 (mp0) outliers start: 34 outliers final: 16 residues processed: 385 average time/residue: 0.5340 time to fit residues: 238.4398 Evaluate side-chains 368 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 345 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 520 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 205 optimal weight: 0.3980 chunk 189 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 213 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 188 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 157 optimal weight: 0.0070 overall best weight: 0.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 637 GLN C 91 ASN C 637 GLN D 91 ASN D 637 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.200374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.135388 restraints weight = 20577.424| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.84 r_work: 0.3309 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3152 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (24 function evaluations) r_final: 0.3152 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 21920 Z= 0.105 Angle : 0.520 7.859 29436 Z= 0.262 Chirality : 0.039 0.179 3204 Planarity : 0.004 0.040 3552 Dihedral : 14.194 132.453 4714 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.47 % Allowed : 16.68 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.17), residues: 2432 helix: 1.33 (0.14), residues: 1460 sheet: -0.49 (0.61), residues: 76 loop : -0.64 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 146 TYR 0.011 0.001 TYR A 328 PHE 0.009 0.001 PHE C 493 TRP 0.007 0.001 TRP C 593 HIS 0.003 0.001 HIS D 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (21920) covalent geometry : angle 0.52023 / 0.26 (29436) hydrogen bonds : bond 0.04130 / 2.74 ( 1010) hydrogen bonds : angle 3.77673 / 2.58 ( 2922) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 365 time to evaluate : 0.582 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.6562 (OUTLIER) cc_final: 0.6221 (tm) REVERT: A 93 GLU cc_start: 0.7262 (mp0) cc_final: 0.6489 (mp0) REVERT: A 96 MET cc_start: 0.5510 (mtm) cc_final: 0.5068 (mtm) REVERT: A 131 ASN cc_start: 0.6824 (m110) cc_final: 0.6428 (m-40) REVERT: A 177 GLU cc_start: 0.7167 (mp0) cc_final: 0.6843 (pm20) REVERT: A 379 THR cc_start: 0.7205 (OUTLIER) cc_final: 0.6989 (p) REVERT: A 535 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7646 (mt-10) REVERT: A 588 GLU cc_start: 0.8032 (pt0) cc_final: 0.7816 (pt0) REVERT: A 591 GLU cc_start: 0.7940 (pt0) cc_final: 0.7570 (mp0) REVERT: A 608 LEU cc_start: 0.7439 (mt) cc_final: 0.7222 (mt) REVERT: A 610 ARG cc_start: 0.6329 (tpt170) cc_final: 0.6004 (tpt170) REVERT: A 618 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7686 (mt) REVERT: B 51 LEU cc_start: 0.6581 (OUTLIER) cc_final: 0.6256 (tm) REVERT: B 93 GLU cc_start: 0.7200 (mp0) cc_final: 0.6412 (mp0) REVERT: B 96 MET cc_start: 0.5510 (mtm) cc_final: 0.5052 (mtm) REVERT: B 131 ASN cc_start: 0.6799 (m110) cc_final: 0.6470 (m-40) REVERT: B 177 GLU cc_start: 0.6978 (mp0) cc_final: 0.6638 (mp0) REVERT: B 458 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8563 (mt) REVERT: B 535 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7707 (mt-10) REVERT: B 591 GLU cc_start: 0.7914 (pt0) cc_final: 0.7576 (mp0) REVERT: C 93 GLU cc_start: 0.7263 (mp0) cc_final: 0.6513 (mp0) REVERT: C 96 MET cc_start: 0.5474 (mtm) cc_final: 0.5032 (mtm) REVERT: C 131 ASN cc_start: 0.6825 (m110) cc_final: 0.6468 (m-40) REVERT: C 177 GLU cc_start: 0.7143 (mp0) cc_final: 0.6694 (mp0) REVERT: C 458 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8570 (mt) REVERT: C 535 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7692 (mt-10) REVERT: C 591 GLU cc_start: 0.7922 (pt0) cc_final: 0.7550 (mp0) REVERT: D 93 GLU cc_start: 0.7066 (mp0) cc_final: 0.6709 (mp0) REVERT: D 96 MET cc_start: 0.5538 (mtm) cc_final: 0.5125 (mtm) REVERT: D 110 MET cc_start: 0.7082 (mtt) cc_final: 0.6771 (mtt) REVERT: D 131 ASN cc_start: 0.6816 (m110) cc_final: 0.6436 (m-40) REVERT: D 177 GLU cc_start: 0.7125 (mp0) cc_final: 0.6712 (mp0) REVERT: D 458 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8561 (mt) REVERT: D 535 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7726 (mt-10) REVERT: D 588 GLU cc_start: 0.7968 (pt0) cc_final: 0.7707 (pt0) REVERT: D 591 GLU cc_start: 0.7928 (pt0) cc_final: 0.7553 (mp0) REVERT: D 610 ARG cc_start: 0.6405 (tpt170) cc_final: 0.6094 (tpt170) REVERT: D 612 LEU cc_start: 0.6983 (OUTLIER) cc_final: 0.6725 (mp) outliers start: 31 outliers final: 16 residues processed: 392 average time/residue: 0.5196 time to fit residues: 235.9378 Evaluate side-chains 371 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 347 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 612 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 32 optimal weight: 8.9990 chunk 148 optimal weight: 0.4980 chunk 10 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 236 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 200 optimal weight: 8.9990 chunk 112 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 203 optimal weight: 8.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 ASN A 118 GLN A 122 HIS A 637 GLN B 91 ASN B 122 HIS B 637 GLN C 122 HIS C 174 ASN D 91 ASN D 118 GLN D 122 HIS D 637 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.196888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.132352 restraints weight = 20491.982| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.93 r_work: 0.3238 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 27 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 21920 Z= 0.155 Angle : 0.589 8.052 29436 Z= 0.293 Chirality : 0.042 0.191 3204 Planarity : 0.004 0.040 3552 Dihedral : 14.667 139.780 4714 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.28 % Allowed : 17.25 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.17), residues: 2432 helix: 1.27 (0.14), residues: 1464 sheet: -0.64 (0.60), residues: 76 loop : -0.64 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 180 TYR 0.015 0.002 TYR D 328 PHE 0.013 0.001 PHE B 537 TRP 0.009 0.001 TRP B 495 HIS 0.003 0.001 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (21920) covalent geometry : angle 0.58938 / 0.29 (29436) hydrogen bonds : bond 0.04954 / 3.27 ( 1010) hydrogen bonds : angle 3.88281 / 2.65 ( 2922) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9141.03 seconds wall clock time: 155 minutes 49.57 seconds (9349.57 seconds total)